1RMH

RECOMBINANT CYCLOPHILIN A FROM HUMAN T CELL

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 

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This is version 1.3 of the entry. See complete history. 


Literature

Crystal structure implies that cyclophilin predominantly catalyzes the trans to cis isomerization.

Zhao, Y., Ke, H.

(1996) Biochemistry 35: 7356-7361

  • DOI: 10.1021/bi9602775
  • Primary Citation of Related Structures:  
    1RMH

  • PubMed Abstract: 

    • The crystal structure of human recombinant cyclophilin A complexed with a substrate of succinyl-Ala-Ala-Pro-Phe-p-nitroanilide (AAPF) has been determined and refined to an R-factor of 0.189 at 2.4 A resolution. The structure revealed only the cis form of the substrate bound to cyclophilin A in a stoichiometry of 1:1 ...

    The crystal structure of human recombinant cyclophilin A complexed with a substrate of succinyl-Ala-Ala-Pro-Phe-p-nitroanilide (AAPF) has been determined and refined to an R-factor of 0.189 at 2.4 A resolution. The structure revealed only the cis form of the substrate bound to cyclophilin A in a stoichiometry of 1:1. This binding ratio is different from the structure of cyclophilin A complexed with the tetrapeptide N-acetyl-Ala-Ala-Pro-Ala-amidomethylcourmarin. Model docking revealed that the trans form of AAPF does not fit into the active site. The observation that only the trans cis form of AAPF binds to cyclophilin A implies that cyclophilin A predominantly catalyzes the trans to cis isomerization of a peptidylprolyl amide bond. On the basis of the structure, it is proposed that Arg55 hydrogen-bonds to the nitrogen to deconjugate the resonance of the prolyl amide bond and thus facilitates the cis-trans rotation.

    Organizational Affiliation: 

    Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill 27599, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYCLOPHILIN AA, B164Homo sapiensMutation(s): 0 
Gene Names: CYCLOPHILIN, PPIA, CYPA
EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P62937 (Homo sapiens)
Explore P62937 
Go to UniProtKB:  P62937
PHAROS:  P62937
GTEx:  ENSG00000196262 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62937
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
AAPF PEPTIDE SUBSTRATEC, D6N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.8α = 90
b = 109.2β = 90
c = 118.7γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 1995-07-31 
  • Released Date: 1996-10-14 
    • Deposition Author(s): Zhao, Y., Ke, H.

Revision History  (Full details and data files)

  • Version 1.0: 1996-10-14
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other